I have some documents that require extensive use of BibTeX files, and on the windows version of TeXworks there is the possibility of running pdflateX+MakeIndex+BibTeX, which is not present in the linux version (I am using ubuntu). I have to separately run BibTeX and the LaTeX compilers so that I can update my citations, which is a bit of a hassle. Is there any way to manually add the pdflateX+MakeIndex+BibTeX mode to TeXworks under linux?

MiKTeX on Windows includes a program called texify which does the combined pdfLaTeX, MakeIndex and BibTeX run. There is not an identical program on Linux, but there are several scripting systems for LaTeX. As Herbert has said, you could write a simple script to do the job, but if you are not a scripting person might want to look at for example latexmk (which just 'does stuff') or arara (which is more user-controlled).